The Trainer Takeover
by NightwingNinja17
Summary: An evil long thought to be dead arises once more to rear its ugly head. And now he's got eyes set on our hero with nothing to stand in his way. After all, who would stop a man who was thought to be dead? What does this mean for our hero and what must he do to stop the impending doom?
1. Chapter 1

Darkness. That's all he felt as he entered the cold, interior room that was his office. He turned on the light, illuminating the walls that were covered in articles of various Pokémon and trainers that he had been tracking all these years. It never ceased to amaze him how often these certain people were in the press.

He then lumbered over to the desk after marveling for what seemed like hours at an object that was just sitting there, front and center, in the middle of a, large, white notepad that was also sitting in the middle of the desk.

And that object was a picture.

Now this was no ordinary picture. It was the picture he had been taking a particular interest to. It was a newspaper article that he had sent to him from the Alolan Islands, talking about the students of a Pokémon school that was in the area and how they'd been able to achieve great things in the last couple of months. But only one thing had caught his eye.

He read over the article attached to it and found that this young man had been attracting the attention of the Alolan Island guardians. This came to no surprise. The boy had a way of attracting the strangest of creatures to him. But these Alolan guardians didn't come to attack him, they came and befriended him.

And that's exactly what he had taken an interest to. This boy he had known all too well. This boy was one of the many, if not the main person who had destroyed his chance at world domination. It was in the blink of an eye that Zygarde had come to his aid and that many others followed suit.

He wasn't bitter or nothing.

Or at least he pretended not to be bitter.

But now it was time to enact a new plan. Something that not even this boy, who could gather all Pokémon of to himself like a moth to a flame, would see coming.

He felt a smile creep onto his lips, reveling in the fact of what was about to happen.

The million-dollar question was how in the world was he going to even entice this boy into a trap he couldn't get out of? Especially since he was in a completely different region then he had ever gone before. This part had him frustrated and it caused him to want to punch something.

Since he didn't have something to punch, he decided that it was best to throw his fists into the top of his desk.

In this mad rush of fury, everything shook as his fists met the wood. Nothing would stop the rage from flowing.

That is until a Greninja figurine fell off the desk and broke.

Luckily, it wasn't a bad break. Something that could be easily fixed with a bit of glue. But then it dawned on him…

" _The boy had a Greninja didn't he?"_ He could only assume since the article talked about this boy having regional Pokémon that he had left some of the ones he had captured here in Kalos. This was the only explanation.

He abruptly turned to face the wall of photos and realized that he had been tracking the movements of said Greninja ever since he found out of its trainer's absence. It made him happy at the chance to capture it once more, but he also knew this wasn't going to be easy.

This was no ordinary Greninja.

He tried tracing the string trail from one end of the wall to the other, but grew confused as the lines intersected more than he thought they would. There was no real connection to a location. This Pokémon was too active.

He then realized though that even in the erratic mess that was the traveled path, there was always one connecting point.

The Lumiouse City Gym.

The thought of being so close to this famed Greninja created much excitement in him and he quickly turned to a nearby computer to check something out.

He quickly made it to the Lumiouse City website and found a ton of pictures of the gym. But it wasn't the location that he needed, he wanted to know who the gym leader was.

It took him a couple of minutes to find out how to discover anything else out about the Gym. When he did find out who the gym leader was, it felt like his heart did a flip inside his chest.

" _The gym leader is still Clement,"_ The one who had destroyed his mind control device and stopped the other Zygarde from destroying the city.

In pictures he found, he saw a robot who he couldn't quite identify, a young girl who he could only assume was his younger sister Bonnie, and he saw a bunch of Pokémon. He was surprised to find though that one of the Pokémon he saw was the very same Greninja.

He now knew he had to do.

And that was to capture this Greninja. Or at least scare it to the point where he could use it as bait to lure its trainer in.

" _Nothing is going to stop me from making you my own this time,"_ He took out a knife that had been sitting in a drawer and stabbed it through the picture in the article. It was of a young boy with jet black hair and on his shoulder, rode a Pikachu, " _I will take you and then my plan for world domination will once again reign supreme!"_

A laugh escaped from his lips. And it wasn't your run of the mill laugh, NO!

It was the laugh of a man who knew what he had to do and what he wanted.

And this time, nothing was going to stop him.


	2. Chapter 2

**Chapter 2:**

 **3 Weeks Later…..**

It had been a long day at the Alolan islands. The students of the Pokémon school were spending their evening by the beach training. But this wasn't any ordinary training.

They were running the length of the beach for an annual local competition.

It was almost like a relay race of sorts, where the trainer couldn't ride any rideable Pokémon, but they had to travel with them. Where the track mostly went around in circles. Each lap the course changed locations. It was a way that the young trainers of the islands could get together and participate in a competition.

And when there was a competition involved the students of the Pokémon academy were sure to follow

"No fair Ash!" Sophocles had to stop and catch his breath, "Can't you just slow down?"

"Sorry! I can't lose this!" Ash had the lead, followed closely by two people who he didn't know.

Ash dashed forward with Pikachu by his side. It felt like old times when they would constantly go running around for miles without a care in the world.

"Pikachu!" Pikachu was so excited to be running alongside Ash and the beach that he had to squeal in delight.

" _And here we have the Kanto native Ash Ketchum in the lead with his pal Pikachu, followed closely by…"_ Ash didn't hear anything else but jumped for joy. He could see the finish line on the top of the hill.

"And we have our winner! It's Ash from the Pokemon school!" Everyone burst out into cheers, whistles and more.

"Pikachu! We won!" Ash ran forward to greet his buddy with a hug and was greeted by happy squeals from the yellow Pokemon.

It didn't take long for the others to follow suit. Mallow and Lana came in Fourth and fifth, Kiawe was in Eighth and Sophocles was dead last. Everyone came into the finish line huffing and puffing.

"Congrats Ash!" Mallow high fived the trainer.

"I didn't know someone could run that fast," Sophocles placed his hands on his knees as he tried to catch his breath.

"I used to train like that with a lot of my Pokemon," Ash rubbed the back of his head as he blushed, "It's no big deal!"

But then the sound of a grumbling belly reached everyone's ears.

"Sorry guys! I've got to run home!" Sophocles gathered his belongings and his Pokemon, "My mom promised me my favorite meal after the race."

"I've got to go too," Lana had already started to walk away, "I promised my mom I'd help put my siblings to bed."

Everyone soon said their goodbyes and all went their separate ways.

"Some race huh?" Kikui walked up to Ash, "You smoked those guys out there!"

Ash just laughed and accepted a high five from the Professor.

"Thanks Professor! Glad you were there to see it," Ash

"Hey, I have to run by the school for a last-minute meeting. Do you mind going home by yourself?" Kikui held out the house key for Ash to grab.

"Sure thing, Professor!" Ash grabbed the key and ran off toward the house leaving a smiling Kikui behind.

Ash sure did enjoy the atmosphere of the Alolan Islands. It was peaceful, calm and the nature made it one of the most beautiful places he'd ever traveled. It was like a warm blanket had been cast over his soul that he had never experienced before.

Even as the night sky had appeared after the breath-taking sunset, he marveled at the many stars he could see. It beat anything he had ever seen before, give or take the many interactions he had with legendary Pokemon some people would only dream of seeing, let alone interacting with.

It didn't take long for Ash to make it back to Kikui's house. When he entered the door of the house he let out the biggest yawn he thought he'd ever let loose.

"Man, I must me more exhausted then I realized," Pikachu chirped his agreement and skittered across the floor to the nearby couch.

Ash then tried to turn on the lights, but they didn't come on. Confusion settled as he tried it again, but this time, a chill ran up Ash's spine.

Pikachu noticed how still Ash was and voiced his concern.

"I'm alright Pikachu. Just going to go step outside and check the fuse box," Ash turned toward the back door and made his way to the breaker box, "I'll be right back buddy."

Pikachu chirped happily and soon Ash was out the door.

When he arrived, it seemed like nothing happened. No lines were cut, nothing seemed out of place and nothing seemed tampered with.

" _So, what caused the power outage?"_ Rustling in the bushes behind the house caught his attention, followed by a familiar sensation. It was one of being able to see through another's eyes, trailed by a connection to a strong bond.

He recognized that bond!

With a gasp, Ash quickly closed his eyes and soon found himself looking through the eyes of another. It showed that he was in a clearing, surrounded by forests all around. In the clearing were flowers that were growing there. Blue ones that seemed to shimmer in the arising moonlight. Ash knew exactly where that was as he often went with Pikachu to clear his head after a long day of school or training.

" _I'm coming!"_ He used his mine to try and communicate with the Pokemon he had a feeling was on the other side listening in.

Ash rounded the path and he stopped. Something didn't feel right. A darkness crept into his soul and mind, one that he had not experienced before. It made the temperature inside of his body drop and Ash grew colder than normal from the rather warm night.

He decided that it was probably for the best that he take it slow.

"Hello? Anyone out there?" Ash cupped his hands around his mouth to try and make his voice sound louder. First there was no reply then there seemed to be the faint sound of someone or something struggling, "Hello?"

And then the reply he received froze him to the ground.

It was Greninja calling. And it wasn't just some run of the mill Greninja.

It was his.

Ash broke free from the freeze and rushed forward toward the clearing, taking great care not to trip over anything. He soon found himself inundated with the smell of the flowers that bloomed there. This confirmed that he was heading in the right direction.

Soon Ash was blinded by the moonlight as the tress parted and he found himself in the clearing. Ash stopped at the edge of the clearing, looking for the source of the outcry; his eyes soon landing on a Greninja trapped in a net that seemed to shock him every once in a while.

"Greninja!" Ash darted forward and started to untangle his friend from the net. This only resulted in getting shocked away from the water Pokemon, "What's going on?"

Greninja tried to explain what had happened to him. How some evil people came and attacked him while he was spending time with Bonnie and Clement, and then a person he thought he recognized had managed to hit him with stun spores. He was the subsequently knocked out and when he woke he was in this field.

"Did you get hurt?"

Greninja shook his head. The only thing that hurt him was the stun spores.

"I've got to get you out of here!" Ash darted forward again and then once again tried to free his friends from the confinements of the net.

"I wouldn't do that if I were you!" Ash quickly whipped around but couldn't see the source of the voice.

But he soon felt the effect of something.

Bolas soon wrapped themselves around his feet and around his torso causing him to fall down. Ash desperately tried to free himself but wasn't successful.

Greninja even tried to free himself as well, wanting so very much to help his now entrapped trainer.

"Get him on his knees!" All of a sudden at least five other people dressed all similarly to each other came from the shadows and surrounded Ash. Two of the more burlier men took Ash by the shoulders and very roughly and painfully had him sit in a position sitting on his knees. Ash struggled against the vice grip hold of these men and didn't stop, no matter how painful it got.

"It's been a while hasn't it Ash?" Ash stopped struggling and turned toward the sixth person who walked up to him. This man had red hair that was buzzed on the sides but then pulled back into a pony tail. He even wore sunglasses that obscured his eyes from anyone.

"How do you know my name?" Ash resumed his struggling, but swiftly stopped when then hands holding him down started to crush his shoulders.

The man knelt down and drew closer to the vulnerable trainer. Greninja called out in terrified croaks letting Ash know that this man meant business.

"I should have known that even when I tried to control you in Kalos that you would forget about me," The man lowered his glasses to expose his eyes.

In recognition, Ash lost all the will to struggle and pulled his legs out from underneath him. He just stared at the man in front of him for a few seconds, only to be replaced by anger with a slight mix of fear.

"Lysandre! But I watched you fall into the rock explosion!" Ash tried to back away, but soon backed into two other men that had followed this crazy man here.

"I did! But in the blink of an eye, some Pokemon caught me and whisked me away," Lysandre did nothing but sit and glare at Ash.

"Well then, what is it that you want with me and Greninja this time?" Ash resumed his struggling.

"Well, if I were to tell you that then where would the fun be?" Lysandre turned to the fifth person and grabbed a rag that had been held out to him. He then rubbed it in between his fingers, "But like my old man used to say, you can be knocked down, but it doesn't mean you're out (Jud Nelson)."

And with that Ash's mouth and nose were covered in the rag that Lysandre had been given. Almost immediately Ash felt his mind start to swim, with there being a simultaneous battle over the control of his muscles and movement.

Ash could feel one of Lysandre's hands in front holding the rag in place and the other was behind his head keeping him from moving it. With nothing else to do, Ash began to make noises in hopes that someone would hear him before the effects of whatever was on the rag started to take hold.

"Shhhhhhhh…There's no need for that here!" Lysandre pressed harder on Ash's face taking immense pleasure in the boy's discomfort, "Just breath in nice deep breaths."

Lysandre smiled creepily as he could tell the boy was losing the battle to stay conscious quickly. Very little noise came from his vocal chords and his eye lids began to droop. He could also feel the muscles in Ash's neck begin to relax.

Ash felt the contents of the rag begin to ravage his conscious mind. It was becoming too much. He vaguely remembered being shushed, and being told to take deep breaths, which was he relaxed was forced to do so. He then felt fingers caress his face causing him to relax further.

"Just like a moth to a flame," Lysandre whispered into the ears of Ash, "You always did have a big heart for Pokemon. Mark my words, this will be the death of you."

And with the sound of Greninja's anguish filled cries, Ash fell into the dark confines of unconsciousness.


	3. Chapter 3

**Chapter 3:**

"Do my eyes deceive me?" Xerosic, the scientist behind all of Team Flare's inventions, exited a helicopter that just landed. It was their ticket off this god forsaken island, "You caught him?"

Lysander just smiled at the antics of the inventor.

"Did you bring what I requested?" Lysander turned toward the copter, looking for the device in question.

"I did," Xerosic sidestepped to get out of his boss' way and behind him sat a gurney that would hold Ash until they got back to their headquarters, "Fit with adjustable clamps on either side of the bed, that not only adjusts up and down but will also adjust to fit the head and neck regions as well."

"Excellent!" Lysandre knelt down to where he now stood over Ash's prone body. Never had the boy looked so much younger than he did right now. The relaxed features of his entire body contrasted greatly with the image Lysandre had in his head of the determined, very tense boy who he had fought many times. It was totally a surreal experience, "Bring it closer so that it's easier for me to get him on it.

Team Flare's resurrected leader knelt down and picked up the young, but phenomenal trainer in his arms, bridal style. But Lysandre struggled with it quite a bit. Ash's arms dangled from his sides, swinging with the sway of the enemy's gate. It took Lysandre every ounce of strength not to fall over as he helped to close the distance between himself and his trusty inventor with the dead weight in tow.

Lysander guided Ash's body to the gurney and Xerosic began strapping him in.

The first step was securing Ash's head. Lysandre achieved this by simply holding the bottom of the boy's chin and used the boy's chest as a stabilizer. Then Xerosic came in with the device that he made and basically made a head restraint, immobilizing Ash's prone head even more. The scientist made sure that those restraints were tight, to not only prevent further injury, but also to keep the kid looking at them should he awake during the journey to headquarters.

They continued this until all the straps and stabilizers had been placed, leaving Ash's body sandwiched between the blocks on either side of him.

Ash was now the official captive of the new Team Flare.

Lysandre then followed his crew into the helicopter. It was much like the last trip that they made when they captured Ash in Kalos. Only the circumstances of Lysandre's need for the boy and his Greninja were different.

You see it remained the same that Lysandre wanted to take Ash's bond phenomenon with Greninja over once more, but the reason behind it was different. He had discovered that he could combine the powers of legendary Pokemon with that of ones who exhibited the bond phenomenon traits. It was like a lightbulb went off in his head.

So, he had Ash tracked after he left Kalos.

Lysandre watched as the boy went back home to the Kanto region and then was surprised that shortly after his arrival back home, he was on the road again. And it was to a region that Lysandre had never heard of before. Lysandre decided that in his best interests, he would build his new headquarters there.

Then the reports started coming in on how Ash had seemed to attract the interest of the island guardians. These were four of them with immense power that he wanted to take control of himself.

And he now had the perfect conduit to do so.

Once the copter rose into the air, everything grew still inside of the vehicle.

It was like all the energy of everyone had been snuffed out by some big battle that wasn't actually waged.

But all that stillness was soon interrupted when Greninja was drug into the main compartment. It had laid eyes on Ash, his trainer and started to get extremely angry.

"Calm down! Nothing has happened to him! He just passed out is all," Lysandre walked over to the Pokemon in front of him. Greninja had been restrained to the point that he was completely paralyzed. No one wanted to see the wrath of the water Pokemon, especially now that it had been reunited with his trainer.

It took them two hours before they arrived back at Team Flare's Alolan headquarters. Everyone exited the aircraft and soon found themselves back on solid ground.

"Lysandre what do you want us to do with him?" Xerosic pointed back towards the gurney holding Ash down.

"Put him in one of the medical observation rooms until he wakes," Lysander also pointed back toward the base, "Make sure to monitor his vitals and alert me when… well you know what."

"And what of Greninja?" The cage with the desperate Pokemon was taken of the chopper and soon trainer and Pokemon were reunited next to each other as captives of one of the worst enemies they had encountered yet.

Xerosic just bowed and prepared the crew to do just what Lysander asked.

 _"_ _This is all going to plan! And soon Ash, soon Greninja, I will have control of you and nothing will stop it now!"_

* * *

Back at Professor Kikui's house, a very worried Pikachu paced the floor while the professor talked to Officer Jenny.

"When was the last time you saw Ash?" Officer Jenny pulled out a pen from a pocket in her vest and prepared to write down the information on a piece of paper that she had sitting in her lap.

"The last I saw of him, we had parted ways. I had to go to the school to check up on something and he was coming home," A very worried professor messed with his hat, feeling utterly helpless.

"What did you find when you arrived back here?"

"I found that the power was out and went to check the breaker box, and that's where I found his hat," Kikui took Ash's hat from its resting place beside him and showed it to the officer.

"I see," She put the pen back in her pocket and stood up, "If I find anything I'll be sure to…."

At that very moment, there was a knock at the door. Kikui stood up too and walked to the front door to find his students standing there.

"What are you all doing here?" Kikui opened the door to let them in and found that there were two strangers in the mix.

"These two," Kiawe gestured to the two blond headed strangers in their midst, "Had something to tell Ash, but with everything that has happened..."

Kiawe let it hang in the air. The tension and fear was so palpable, that it seemed like one could cut it with a knife. Pikachu recognized them though and quickly perked up and ran toward the youngest of the two blond headed people in the room.

"Hello Pikachu! How are you?" She rubbed his cheek and Pikachu let out the cutest squeals of delight.

"And who might you two be?" Kikui gestured for them to sit on the couch next to him.

"Hi! My name is Clement and this is my little sister Bonnie!" Bonnie waved excitedly at everyone, "We are friends of Ash from the Kalos region."

Everyone seemed excited at the mention of the Kalos region.

And everyone seemed to pester the Kalos due with a bunch of questions.

"He guys, they are our guests," Kikui tried to calm his rambunctious students, "I'm sure they will answer your questions at any time. Just right now isn't that time."

"Didn't the region have a crisis with a legendary Pokemon a while back?" Sophocles sat back down seemingly very interested in what was going on.

"Yes. And that's why we are here. Ash may be in great danger!" Clement adjusted his glasses to fit more comfortably on his face, "You see back when Ash was with us in the Kalos region, there was an organization that came into power called…"

"Team Flare," Bonnie crossed her arms and tried to look angry.

"Right. You see the leader of Team Flare wanted to take over the world using the power of a legendary Pokemon called Zygarde."

"Zygarde?" Everyone's eyes simultaneously grew wider.

"Yes. Zygarde is the protector of the Kalos region and is a very powerful Pokemon. During our journey, we befriended one of his many pieces and it made us targets. But anyway, the leader took a liking to Ash and at one point from what he told us after the incident is that he tried to take over Ash's mind alongside one of his Pokemon he caught while in our region."

"But Ash defeated this guy, right?" Kiawe grabbed fistfuls of his hair in a surprised manner.

"Ash didn't bend to his wished, did he?" Lana let Poplio down and it bonded over to Bonnie who started stroking it.

"He was successful in not bending at all," Bonnie jumped up from her position beside her brother, fist in the air, "And he did defeat the guy!"

"Or so we thought. Months after the incident and after Ash had left the Kalos region to go home to the Kanto Region, we found out that a Secret Organization known to protect Kalos and enforce the law had captured and imprisoned the leader and any others were part of the cause, in a highest security prison in the region."

Everyone was staring at Clement, letting a tense silence fill the room.

"But this is why we think Ash is in danger. A couple of weeks ago, there was a breakout and the leader, along with a handful of his men. They also managed to re steal the technology behind the mind control that they tried to use on Ash the first time."

"We also know that one of Ash's Pokemon got captured by this man and his crew," Bonnie folder her arms over her chest, "And we know this because it happened right in front of us."

"No way!" Lana and Lillie both gasped in surprise at the exact same time.

"It's no ordinary Pokemon either. It was one Ash managed to form an extremely powerful bond with. And because of this bond, both Pokemon and Trainer could experience a transformation very equivalent to Mega- Evolution."

Everyone's gaze seemed to flit back and forth between the Kalos duo, not knowing whether or not to believe what they were hearing.

"Then if what you are saying is true, we need to find Ash quickly." Everyone turned to Clement.

"We not only have to find Ash quickly, but we have to find him now or else, I fear for his survival."


	4. Chapter 4

**Chapter 4:**

Disorientation. That's all Ash felt as he slowly woke up. It felt like he was underwater. Unable to really hear, see or breathe for that matter. He sluggishly made an attempt at opening his eyes and found them to be almost non-functioning. He was also dizzy which was only made worse by movement. This scared Ash and he usually didn't scare easily.

He tried to move his arms, but felt them held fast to his sides. Ash then tried to move his head to look around, but found that he couldn't move his head either. Something cold and hard pressed against his ears almost painfully. Also, there was a strap that rested across his forehead allowing the blocks on either side of his head to be practically immovable.

He startled himself when his fingers brushed up against something soft. He used what little of his fingers he could move to stroke the underside of whatever was on top of him and found it to be a blanket.

Ash then noticed the smell. It was sterile and almost like he had been in some sort of medical wing. Ash managed to open his eyes just a bit to make out the white walls and the blazing white light shining down on him. This confirmed in his own mind that he was exactly where he thought he was.

The young trainer was in a medical wing of some facility.

This realization caused Ash to resume his struggling against the restraints.

Ash quickly stopped struggling however when he heard the sound of voices. Muffled as they were, he could make it out to be talking about some sort of device that someone else had made. Tried as he might, he used what little hearing he had to try and listen in on the conversations going on around him. But was only successful in sneezing, alerting the others in the room to his presence.

"He's awake," someone nearby lowered the blanket that had been placed around his shoulders to where the top of his chest was exposed. The person now standing above him adjusted something attached. This caused the sound of beeping from another device nearby to ring loudly in Ash's ears.

"Can you hear me?" A guy wearing goggles and appeared to have a small ponytail sticking straight up from the top of his head.

It was still muffled.

"A little bit," Ash gasped in surprise when he realized how slurred his voice had become. He couldn't remember what had happened to lead up to these events.

"You'll be talking like that for a while," The man voice started sounding extremely familiar and Ash tried to jog his memory to attempt to try and figure out why though.

The cold of the room began to get to Ash. He began to realize that he no longer had his shirt and jacket on. Now the only thing sheltering him from the cold was his own body and what little blanket was still covering him.

"Lysandre sir, he has awoken!" The com system in the room lit up with the sound of the familiar voice.

" _Good! Bring him to holding chamber one! And bring him in without the stretcher,"_ Everyone in the room rallied around the bed Ash was laying on and began to unhook straps and blocks restraining the young boy. Ash quickly sat up, even though he was as shaky as a leaf about to fall off a tree, but was met with a wave of dizziness that engulfed him to the point of nausea.

He was then roughly taken off the stretcher which didn't help matters any. He almost collapsed as soon as his own weight was placed on his legs and feet. If it wasn't for the two men holding him firmly by the arms, he probably would have fallen to the ground. Ash felt the unease and panic begin to rise when the crew around him began to almost drag him out of the room and into the long hallway to who knew where.

Ash's nerves lessened slightly when he could feel the effects of whatever had knocked him out begin to dissipate. It was like he had been stuck with a basket on his head and now he was allowed the freedom of being completely aware of his surroundings.

But he didn't want them to know that.

So, he allowed himself to be almost dragged into the room they were bringing him to. \

The feeling of freedom didn't last long however, for when Ash entered the new room, there stood Lysandre. And next to him, strapped into some device, was Greninja. The water Pokemon made eye contact with Ash, he looked terrified.

"Nice of you to join us!" Lysandre called out from the other side of the room.

Ash just froze. He didn't know if it was more from terror of seeing Lysandre again or the fact that one his Pokemon was now strapped down and at the mercy of this monster of a person.

"Let him go!" Ash ripped his hands from the men's' grasp and ran a bit forward. He was pursued by them, but with a hand gesture from Lysandre, they stopped.

"Why Ash! I don't plan on doing that. Why don't you come over here and see what I've created!"

Ash's curiosity was peeked, but not enough to want to go over there, next to his kidnapper. But one of the men behind him pushed him forward not allowing there to be anymore hesitation from the trainer in front of them.

He slowly made his way over, stopping only once to glance over at Greninja. Greninja seemed to be just as terrified as he was which, for some odd reason, brought comfort to Ash.

He was glad he wasn't the only one scared.

"Isn't it beautiful?" Lysandre held his hands out towards an object obscured by some sort of tarp. But it soon fell off to reveal a device not unlike the one that Lysandre tried to use on Ash during the last time Ash was captured by the man.

Ash instinctively backed up. He wanted nothing to do with this.

So, Ash turned and ran away.

"What should we do?" Xerosic walked up to his boss.

"I've got this," And soon Lysandre was following Ash.

With a few quick strides, Lysandre soon had caught up to the fleeing trainer. He didn't think about it, but he lashed out and punched the boy square in the face. This stunned the boy enough to where Lysandre could pin Ash's arms in a crisscrossed manner against the boy's chest almost as if the boy was hugging himself. He allowed him to struggle a bit and even heard a few times Ash demanded Lysandre to let him go, but nothing was going to change his mind. Lysandre reveled in the closeness of his captive. He wasn't about to let Ash go that easily.

"Let Greninja go!" Lysandre turned himself around to where Ash was now facing his own Pokemon. Ash had now changed his tune from asking for himself to be set free, and instead pleaded with his captor to let his Pokemon go free.

Ash had stopped struggling by this point and watched others take a hold of Greninja and lift him out of his confinement. He stood there absolutely confused as to what was going on and so did Greninja.

"Greninja get out of here!' Ash called out to the water Pokemon. But he didn't make a move. He just stared into Ash's pleading eyes not shaking his gaze at all.

"You see, Greninja won't leave." Lysandre pulled tighter on Ash's arms, this time moving his hands to the boy's wrists, "I told him if he tried to escape after I caught you, I'd hurt you."

Ash froze and stood staring at his Pokemon. Greninja was one of his most powerful Pokemon he'd ever caught and now, seeing him reduced to nothing but a pawn was heartbreaking.

"Now let's make this simple, shall we?" Lysandre let Ash go, confident that the boy wouldn't try anything, "You will activate your bond phenomenon with Greninja. If you don't I will hurt you and we all know that hurting either of you causes pain in the other. Am I right?"

Ash couldn't mutter a word in response. He continued to stand there immobile, seemingly almost lifeless. His determination not to give Lysandre what he wanted seemed to be mirrored in Greninja's eyes. Even though without the bond phenomenon, he couldn't feel what Greninja was thinking, but he saw it. And it was enough for Ash to make a decision.

"You've got it all wrong Lysandre!" Ash's voice rose as the anger quelled inside of him, "First we only feel each other's pain when we are synced. And second, you should know by now that we won't be controlled by the likes of you! And we will never continue to do so."

Lysandre smirked. He figured this would be the kid's answer.

"Fine then. We'll do it your way."

Ash heard a whine coming from somewhere, sounding like some electrical device was charging up. He couldn't quite pinpoint the source of the noise.

But as the noise grew louder, he could tell exactly where it was coming from.

It was coming from his wrists.

He looked down and saw two identical, black bracelets strapped neatly to his wrists. He then looked up to Lysandre who he saw was standing near some control panel. Lysandre must have attached them to his wrists when he just had a hold of him.

"Like I said, Pokemon would be the death of you one day," and he hit a button which caused a surge of electricity to pulse from the bracelets and into Ash.

Ash had been hit by many of Pikachu's thunderbolts and electricity before but nothing had prepared him for this.

It felt like a ton of tiny daggers just lightly but at the same time very harshly away at his body. He could feel his muscles tense and relax almost in simultaneous motions that some didn't feel right. This scared Ash to his core.

Ash soon collapsed when the device was turned off and in stride Greninja came running up alongside it's trainer. Ash picked himself up onto his knees only looking into the eyes of the water Pokemon standing in front of him.

"Ash do you agree to my terms now?" Lysandre walked over and knelt in front of his opponent.

Ash just glared. He had no intentions of willingly giving himself, or Greninja for that matter, over to this madman.

"You know our answer!" Ash clenched his teeth in anticipation of what was to come, watching Lysandre's every move after that.

"Very well then!"

And here came the shock.

And it lasted longer this time.

"Alright!" Ash fell on the ground once again due to the lack of control over his own body, "We'll do it!"

The electricity stopped.

"Excellent! I knew you would come around to our way of thinking!" Lysandre's grin grew to twice its original size.

"But first you must tell me what your plan for us is!" With the help of Greninja, Ash stood up, not letting the pain he was feeling get in the way of showing he was strong.

"You promise that you will still go through with it if I tell you?"

"Promise!"

Lysandre's smile turned into a smirk. This boy was a lot smarter than people gave him credit for.

"Well then," Lysandre turned his back towards Ash, "I recently acquired some knowledge that you Ash have the ability to see and use Aura. Now that's not something I've seen a lot in people. Pokemon that's one story, but a human! Man! The possibilities are endless!"

Lysandre now turned towards Ash.

"After I learned that of you, I thought back to our last encounter and in my research, I learned that any Aura user can combine the powers of one of their own Pokemon with that of others. And I thought why not experiment it with you? With your bond phenomenon with Greninja and the power that some certain Pokemon here on these islands possesses, I would be unstoppable."

"You know I would never agree to that!" Ash shot forward in an attempt at attacking Lysandre, but was soon restrained once more by the other members of the New Team Flare that were in the room.

"Ah! But remember we just made a deal!" Lysandre wagged his finger in front of his face, reprimanding Ash's words, "But I had anticipated this sort of resistance, so I had Xerosic here remedy that."

Xerosic grew all excited! His device was sure to work this time and their famed enemy would now be there slave.

"You see that device I showed you earlier is a mind control device. It's the same technology behind what I used on you before, only this time I'm using something much stronger than Mega Evolution energy."

Panic began to arise in Ash. He didn't want to be mind-controlled again, especially not to the likes of Lysandre. But he had no choice. He made a promise that he wouldn't change his mind if he was told of this evil man's plot.

"Now all I need is for Ash-Greninja to appear and we have the beginnings of a human/Pokemon weapon on our hands!"

The men restraining Ash let him go and Ash fell to the ground on his knees.

He could feel the tears welling up in his eyes before he even registered that he was crying. Ash wouldn't put anyone in danger, at least not willingly anyway, but now the rules were changing.

"It's time." Lysandre whispered into

Ash stood up again, with tears streaming down his face, and looked Greninja square in the face. He didn't even know if it would still work as well as the bond worked before Greninja and Ash had departed. But for both their sakes, he would have to try.

Greninja walked up to Ash and put Ash's hands in his. Then the water Pokemon reached over to his trainer's face and wiped a tear off that just fell. This reminded Ash of the times where the two of them would do clasp hands as sign of letting each other know they would do this together. The wiping away of tears was new, but he took it as a sign that their bond never wavered. Even when each other were in distant regions it still remained strong. He smiled, even though it was a small smile at this notion.

"Ready Greninja?"

He croaked his approval.

"Then let's get stronger together once more," Ash let go of one of Greninja's hands and prepared himself for what was to come. He could feel the shroud of water fall over the Pokémon's body and soon he himself was soaked. Then the water abruptly stopped and soon Greninja had a giant water shuriken appear signaling that the transformation was complete.

The sentimental moment was quickly ended however when a beam of red light overcame Trainer and Pokemon. Ash immediately felt an invisible force try to enter his mind and consume it. The caused pain and with the lingering effects of the electricity that he had been previously zapped with it worsened.

"There's no use in fighting it Ash! It's more powerful than you can ever imagine!" Lysandre raised his voice to be louder than the machine.

But his triumph was short lived however when the power to the device cut out leaving some very confused people standing there frozen due to not having the slightest clue as to what was going on.

"Xerosic what's going on?"

"There seems to be a crack in the power core." Xerosic adjusted his goggles to his eyes.

"How long will it take to fix?"

"A couple of hours!" Xerosic rounded the corner to behind the machine, "And that's if I don't find other problems."

"Well get to it then!"

Lysandre was furious. At his moment of victory, it ended in disaster as normal.

And in his mad fury, he let it all loose on Ash who couldn't defend himself.

And the way it ended was Lysandre getting a water shuriken to the face.

The end resulted with Ash sporting a bloody nose, several cuts on his face and arms and what appeared to be an injured wrist due to Ash holding his hand really close to his body. Ash was also sitting on the ground, breathing raggedly, with an angry Greninja standing over him, ready to move if given the command.

"Lysandre what do we do with him?" One of the men pointed toward Ash.

"We're going to let him go!" Lysandre spoke through clenched teeth.

"Let him go?" Xerosic poked his head from behind the mind-control device.

"He's of no use to us right now! And I certainly don't want the authorities finding out of our plans before we enact them."

Lysandre's eyes then fell on Ash and didn't move from the boy. But then he pushed the button and the electricity from the bracelets came to life once more. Ash could do nothing but take it that is until he passed out right in front of everyone. Greninja even faltered and the Ash-Greninja form disappeared. He soon sat next to his trainer, showing that he was exhausted as well, but soon conformed to unconsciousness as well.

"Why Lysandre? If we let him go now then he will still alert the authorities!"

"He doesn't know where we are," Lysandre smirked, "And in reality, it's all going to plan. He will lure the four to us."

Xerosic's smile grew.

"And then we will have the means of taking over the world!"


	5. Author's Note

Hey guys! I am going to be rewriting this story because I feel I have a better idea for it! Hopefully you'll love it as much as you did this one!

Thanks!

NightwingNinja17


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